Variant report

Variant	rs13106574
Chromosome Location	chr4:87769929-87769930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10015508	0.81[TSI][hapmap]
rs13120839	0.89[ASW][hapmap];0.81[TSI][hapmap]
rs13149938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012114	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17012130	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28495376	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28574613	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28682481	0.81[EUR][1000 genomes]
rs34881728	0.91[EUR][1000 genomes]
rs35392566	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4639036	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58866123	0.82[EUR][1000 genomes]
rs62305606	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6811350	0.89[ASW][hapmap];0.81[TSI][hapmap]
rs727143	0.81[TSI][hapmap]
rs72874293	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13106574	AFF1	cis	lymphoblastoid	seeQTL
rs13106574	AFF1	cis	cerebellum	SCAN
rs13106574	PTPN13	cis	cerebellum	SCAN
rs13106574	DMP1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87767000-87771000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:87768000-87770800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:87768200-87771400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:87768400-87770200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:87768800-87770000	Active TSS	Psoas Muscle	Psoas
6	chr4:87768800-87770400	Active TSS	Esophagus	oesophagus
7	chr4:87768800-87770600	Enhancers	HMEC	breast
8	chr4:87769000-87770000	Active TSS	Right Atrium	heart
9	chr4:87769000-87770400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:87769000-87770800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr4:87769200-87770200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:87769200-87770400	Active TSS	Left Ventricle	heart
13	chr4:87769200-87770600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:87769200-87771200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:87769400-87770000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr4:87769400-87770000	Weak transcription	Hela-S3	cervix
17	chr4:87769400-87770200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:87769400-87770200	Enhancers	Brain Angular Gyrus	brain
19	chr4:87769400-87770200	Weak transcription	Brain Anterior Caudate	brain
20	chr4:87769400-87770200	Enhancers	Right Ventricle	heart
21	chr4:87769400-87770400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:87769400-87770400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr4:87769400-87770600	Enhancers	Spleen	Spleen
24	chr4:87769600-87770000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr4:87769600-87770200	Enhancers	Brain Substantia Nigra	brain
26	chr4:87769600-87770200	Enhancers	Placenta	Placenta
27	chr4:87769600-87770600	Enhancers	NHDF-Ad	bronchial
28	chr4:87769600-87771200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:87769600-87771600	Enhancers	Fetal Muscle Trunk	muscle
30	chr4:87769600-87771600	Flanking Active TSS	NHEK	skin
31	chr4:87769600-87776800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:87769800-87770200	Enhancers	Stomach Smooth Muscle	stomach
33	chr4:87769800-87771600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:87769800-87778600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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